tbuckley/cabot-search huggingface dataset:
Abstract 3286: B-hCD94/hNKG2A mice provide a preclinical tool for evaluating therapeutic antibodies targeting human NKG2A
Authors: Chengzhang Shang, Fang He, Mari Kuraguchi, Jing Zhang, Qingcong Lin
Journal: Cancer Research (2023)

Abstract The immune cell checkpoint NKG2A and its coreceptor, CD94, are expressed by many circulating NK cells and by a subset of CD8 T cells in tumors. When CD94/NKG2A recognizes the HLA-E-peptide complex, the protein tyrosine phosphatase SHP-1 is recruited to the signaling synapse, resulting in the delivery of inhibitory signals to the effector cells and inhibition of their immune activities. In preclinical mouse models, blocking antibodies against NKG2A restores the reactivity of these effector cells, resulting in better suppression of tumor growth. Thus, NKG2A targeting is currently being evaluated in the clinic to evaluate tumor cell killing. To evaluate the in vivo efficacy of anti-NKG2A in mice, we successfully generated a humanized CD94/NKG2A double knock-in mouse strain (B-hCD94/hNKG2A mice), in which the mouse CD94 and NKG2A genes are replaced by the corresponding human CD94 and NKG2A genes in situ in cis, respectively. Human CD94 and NKG2A mRNA and proteins were exclusively detectable by flow cytometry in homozygous humanized mice, confirming successful generation of the model. This model was used to demonstrate in vivo efficacy of monalizumab analog in suppressing the growth of MC38 tumor cells expressing human HLA-E (B-hHLA-E MC38). Furthermore, dual blockade of monalizumab and PD-L1 further suppressed B-hHLA-E MC38 tumor growth. Together, these data indicate that this double humanized model is an effective tool for evaluating novel anti-human NKG2A therapies, and warrants the generation of a quadruple humanized model (B-hPD-1/hPD-L1/hCD94/hNKG2A mice) to further evaluate the synergy of drugs blocking each checkpoint. Citation Format: Chengzhang Shang, Fang He, Mari Kuraguchi, Jing Zhang, Qingcong Lin. B-hCD94/hNKG2A mice provide a preclinical tool for evaluating therapeutic antibodies targeting human NKG2A [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3286.
Abstract 149: An organoid model for understanding the pathogenesis of Lynch syndrome
Authors: Caroline Guild, Kirby Madden-Hennessey, Chris Heinen
Journal: Cancer Research (2023)

Abstract Lynch syndrome (LS) is an inherited predisposition for developing cancer caused by germline variants in mismatch repair (MMR) genes. It is estimated that LS is responsible for 1 out of every 35 colorectal cancers and 1 out of every 56 endometrial cancers. Loss of MMR is also seen in many sporadic cancers. Still, the mechanism of tumorigenesis in these patients is unknown. Loss of MMR increases genomic mutation rate, but it is unclear if increased mutational burden alone leads to tumorigenesis. Recent studies of LS patient colon samples show fields of morphologically normal tissue in which cells have lost expression of an MMR protein, suggesting that loss of MMR in these cells is sufficient to confer an advantage over heterozygous cells still proficient in MMR. However, whether MMR loss provides a direct advantage to cell types associated with cancer in LS has not been directly tested. We hypothesize that loss of MMR is sufficient to confer a selective advantage to colonic stem cells and is the first step towards tumorigenesis in LS patients. To test this, we use a human colonic organoid model to examine competition between MMR-deficient (dMMR) and MMR-proficient (pMMR) cells over time. The colonic organoids are differentiated from human embryonic stem cells. To track cell populations, dMMR stem cells are labeled with mCherry and pMMR stem cells are labeled with GFP. We have initially observed that dMMR stem cells are much more efficient at generating colonic organoids. Thus, the cells are mixed so that resulting organoids initially contain a small population of dMMR cells in order to mimic the spontaneous loss of heterozygosity that occurs in LS patients’ colonic crypts. Live fluorescent imaging of individual organoids is used to quantify changes in cell population over time. Preliminary data indicate that dMMR cells can outgrow pMMR cells resulting in a shift in the ratio of green to red cells over a two-week time period. These results suggest that loss of MMR function imparts an immediate selective advantage. Furthermore, this assay could be used to find conditions or compounds that decelerate population shifts with the ultimate goal of finding a way to reduce dMMR fields in LS patients. In these ways, this assay can be leveraged for gaining new insights into MMR function, pathogenesis of LS, and potential therapies for LS. Citation Format: Caroline Guild, Kirby Madden-Hennessey, Chris Heinen. An organoid model for understanding the pathogenesis of Lynch syndrome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 149.
Abstract PL03-04: Forecasting pancreatic carcinogenesis through spatial multi-omics
Authors: Elana Judith Fertig
Journal: Cancer Research (2023)

Abstract This talk presents a hybrid computational and experimental strategy to uncover interactions between neoplastic cells and the microenvironment during pancreatic carcinogenesis. As pancreatic cancer develops, it forms a complex microenvironment of multiple interacting cells. The microenvironment of advanced pancreatic cancer includes a dense composition of cells, such as macrophages and fibroblasts, that are associated with immunosuppression. New single-cell and spatial molecular profiling technologies enable unprecedented characterization of the cellular and molecular composition of the microenvironment. These technologies provide the potential to identify candidate therapeutics to intercept immunosuppression in pancreatic cancer. Inventing new mathematical approaches in computational biology are essential to uncover mechanistic insights from high-throughput data for these precision interception strategies. Here, we demonstrate how converging technology development, machine learning, and mathematical modeling can relate the pancreatic precancer microenvironment to carcinogenesis and therapeutic response. Combining genomics with mathematical modeling provides a forecast system that can yield computational predictions to anticipate when and how the cancer is progressing for therapeutic selection. This mathematical forecast system will empower a new predictive oncology paradigm, which selects therapeutics to intercept the pathways that would otherwise cause future cancer progression. Citation Format: Elana Judith Fertig. Forecasting pancreatic carcinogenesis through spatial multi-omics. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr PL03-04.
Abstract 5862: ABCB5 knockdown suppresses tumor-intrinsic expression of immune checkpoint regulators PD-1 and PD-L1 in hepatocellular carcinoma (HCC)
Authors: Chun Philip Yeung, Brian J. Wilson, Yuzuru Sasamoto, Ana Maria Waaga-Gasser, Svetlana Karpova, Qin Guo, Natasha Y. Frank, Markus H. Frank
Journal: Cancer Research (2023)

Abstract ATP-binding cassette member B5 (ABCB5) identifies cancer-initiating cells (CICs) in multiple malignancies, including malignant melanoma, colorectal cancer, glioblastoma, and hepatocellular carcinoma (HCC). In human melanoma, ABCB5-positive CIC subpopulations have been shown to preferentially express the immune checkpoint molecules PD-1 and PD-L1, and tumor-intrinsic PD-1 receptor functions have been found to promote tumor growth, even in mice lacking adaptive immunity. In HCC, where ABCB5 mediates CIC chemoresistance, PD-1 expression has also recently been identified. However, whether ABCB5 regulates tumor-intrinsic PD-1 expression in HCC or other malignancies is currently unknown. Here, we employed RNA interference in Hep G2 HCC cells with high endogenous ABCB5 expression to study the potential role of ABCB5 in regulating PD-1 expression, utilizing the ABCB5 shRNA target sequence GCTGGAAAGATAGCAACTGAA for ABCB5 knockdown (KD) as described previously. Endogenous ABCB5 levels in ABCB5-KD cells were successfully reduced by 92.8% compared to controls. Investigation of the effects of ABCB5-KD on tumor-intrinsic immune checkpoint molecule expression and on expression of the HCC-CIC marker GRN revealed that ABCB5-KD significantly reduced PD-1 expression by 98.0%, and PD-L1 expression by 62.8% compared to controls. Expression of GRN was also significantly reduced in ABCB5-KD cells by 78.8% compared to controls, suggesting ABCB5 KD-dependent loss of CIC phenotype. Injection of ABCB5-KD cells in NSG mice showed 32.3% reduction in tumor size at endpoint (6 weeks) compared to controls (728.7 ± 199.3mm3 vs 1076.0 ± 450.9 mm3, mean ± SD; p&amp;lt;0.005, repeated measures ANOVA) and 8.53% reduction in tumor weight at endpoint (0.47 ± 0.21g vs 0.51 ± 0.21g, mean ± SD). These results provide initial evidence in an HCC cell line model system that ABCB5 functionally regulates tumor-intrinsic PD-1 and PD-L1 expression. They therefore suggest that ABCB5 blockade represents a novel therapeutic strategy for targeted inhibition of pro-tumorigenic tumor-intrinsic PD-1/PD-L1 expression, with important additional implications for immune checkpoint-targeted cancer immunotherapy. Citation Format: Chun Philip Yeung, Brian J. Wilson, Yuzuru Sasamoto, Ana Maria Waaga-Gasser, Svetlana Karpova, Qin Guo, Natasha Y. Frank, Markus H. Frank. ABCB5 knockdown suppresses tumor-intrinsic expression of immune checkpoint regulators PD-1 and PD-L1 in hepatocellular carcinoma (HCC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5862.
Abstract 43: Application of MiniPDX® in clinical indication identification and anti-tumor drug development
Authors: Yuan Long, Bin Xie, Hongkui Chen, Shizhu Zhao, Le Li, Song Xi, Danyi Wen
Journal: Cancer Research (2023)

Abstract MiniPDX® represents a novel in vivo drug sensitivity test with fast turnaround (7-10 days), using either fresh patient tumor samples or tissues from established PDX models. We systematically evaluated and compared the response rates of MiniPDX® assays and PDX assays pair-wise in 26 PDX models across 3 types of cancers to 12 clinically relevant regimens for chemical and targeting drugs. The results showed a high correlation between drug responses of the two assays, with sensitivity and specificity of 80% and 93%, respectively. More studies of different tumor types showed that MiniPDX drug sensitivity test results were consistent with clinical responses in most patients, which indicated that MiniPDX® models have great potential in guiding personalized cancer therapy. LIDE has completed over 3,000 MiniPDX® tests for clinical precision medicine, covering more than 50 indications. MiniPDX® was used to rank clinically approved drugs or drug regimens to guide the selection of the best individualized treatment strategy. At the same time, screening other compounds facilitates selection of the best drug candidates for further R&amp;D. Importantly, performing MiniPDX® Mouse Trial using fresh tumor samples generated from clinic is beneficial for determination of potential clinical indications. Only thousands of fresh cells leftover from MiniPDX® preparation are sufficient to get genomic and transcription data by OncoVee™ K-cell technology. The combination of MiniPDX® assay and omics data would be very useful for determination of potential bio-markers in order to distinguish responders and non-responders in population with certain indication(s) and leveraged for patient stratification and selection criteria in clinical trial design. Currently, we are developing a new version of MiniPDX® assay for immunotherapy (IO-FIVE, Immuno-Oncology Fast In Vivo Efficacy test) by using fresh patient cancer cells with autologous immune cells to maximally mimic human tumor microenvironment before seeding in immune-deficient mice. Total cell viability and cell phenotyping are tracked before and after drug treatment to evaluate its in vivo efficacy within two weeks. More than 60 samples have been tested and the IO-FIVE functional assay can effectively distinguish the non-responder from responders for immunotherapeutic drugs. Several Investigator Initiated Trials (II-T) are on-going to further validate the correlation of IO-FIVE result to clinic endpoint. Citation Format: Yuan Long, Bin Xie, Hongkui Chen, Shizhu Zhao, Le Li, Song Xi, Danyi Wen. Application of MiniPDX® in clinical indication identification and anti-tumor drug development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 43.
Abstract 2495: Investigating pancreatic cancer-derived extracellular vesicle signaling in the tumor microenvironment
Authors: Jennifer M. Finan, Julie Saugstad, Jonathan Brody
Journal: Cancer Research (2023)

Abstract In many solid tumors, including pancreatic ductal adenocarcinoma (PDAC), the secretion of extracellular vesicles (EVs) has been shown to support tumor progression, chemotherapeutic resistance, and metastasis. Importantly, PDAC tumors are composed of up to 80% non-tumor cells and an extracellular matrix, yet no studies have been performed to determine whether PDAC EVs are imported preferentially by specific non-tumor cell types. To improve our understanding of this signaling, we aim to define the recipient cells of PDAC EVs and evaluate the functional importance of this internalization. Utilizing an in vitro live imaging system, we found that cancer-associated fibroblasts (CAFs) import more PDAC EVs than normal pancreas epithelial, endothelial, or PDAC cells, suggesting PDAC EV trafficking may be preferential to CAFs. We have generated human PDAC and mouse KrasG12D Trp53R172H driven (KPC) PDAC cell lines to express an extracellular particle reporter labeling the inner leaflet of cell membranes with GFP-nLuc. We are currently using this model to characterize recipient cells of the GFP-nLuc-positive EVs in an immunocompetent orthotopic PDAC mouse model. We developed flow cytometry and immunofluorescence panels to assess PDAC EV import by CAFs, endothelial cells, macrophages, B cells, and T cells in developed tumors. Utilizing immunofluorescence staining for a panel of phenotypic markers, we will assess the functional importance of EV internalization. Future studies will begin to determine how EV mRNA cargoes are important for recipient cell phenotypic and functional changes. This study is the first to ascertain the fate of PDAC EVs within the tumor microenvironment in a physiologically relevant model. Citation Format: Jennifer M. Finan, Julie Saugstad, Jonathan Brody. Investigating pancreatic cancer-derived extracellular vesicle signaling in the tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2495.
Abstract 401: Developing KRAS G12C inhibitor-resistant tumor models for efficacy evaluation of next-generation anticancer therapies
Authors: Jun Zhou, Zi Ye, Ning Bo, Dan Zhang, Li Hua, Chenpan Nie, Jingjing Wang, Rajendra Kumari, Leo Price, Xiaoxi Xu
Journal: Cancer Research (2023)

Abstract Background: AMG510, a novel KRAS G12C mutation-specific inhibitor approved in 2021 by FDA, was the first therapy to directly target the KRAS oncoprotein in KRAS-mutant cancers with other direct KRAS G12C inhibitors currently being investigated in multiple clinical trials. However, the emergence of resistance in patients who initially were responsive is a challenge. Uncovering the underlying mechanism of resistance would support the identification and development of novel therapies to overcome drug resistance. In this study, we generated a panel of KRAS G12C inhibitor-resistant tumor models by introducing a secondary KRAS mutation on top of G12C for use as in vitro and in vivo tools to develop possible strategies to overcome such resistance. Methods: First, by using CRISPR/Cas9, we introduced a secondary KRAS mutation, including Y96C, Y96D and Y96S in MIA PaCa, which harbours a homozygous KRAS G12C mutation. Point mutation knock-in was validated by sanger sequencing and cell identity was confirmed by SNP. Then cell viability was measured by CellTiter-Glo after 5 days incubation with AMG510 and MRTX849. RAS-MAPK pathway activity was assessed in the parental and mutant cell lines Y96D by Western blot. Xenograft of MIA PaCa KRAS G12C/Y96D cells l was also established. Results: Successful homozygous point mutation knock-in was achieved as confirmed by sanger sequencing. The double mutant cells displayed the similar growth rate as well as the morphology. In cell viability assays, relative to KRAS G12C parental cells, cells expressing the double-mutant alleles showed marked resistance to AMG510 and MRTX849. Consistent with the effects on cell viability, persistent phosphorylated ERK (pERK) and pRSK levels was also observed in KRAS G12C/Y96D expressing cells even at high concentrations of MRTX849, indicating sustained RAS-MAPK activity. In addition, MIA PaCa-KRAS G12C/Y96D was able to grow in vivo and will be used for pharmacological evaluation of KRAS inhibitors. Conclusion: These double-mutant cells can be used to assess preclinical in vitro/in vivo efficacy of KRAS-targeted therapeutics. Crown Bioscience is in the process of developing a series of KRAS G12C inhibitor-resistant cell lines to better facilitate efficacy testing of KRAS-targeted therapeutics. Citation Format: Jun Zhou, Zi Ye, Ning Bo, Dan Zhang, Li Hua, Chenpan Nie, Jingjing Wang, Rajendra Kumari, Leo Price, Xiaoxi Xu. Developing KRAS G12C inhibitor-resistant tumor models for efficacy evaluation of next-generation anticancer therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 401.
Abstract 5111: VentX-modulated tumor associated macrophages revert immune suppression in tumor microenvironment and promote efficacy of gemcitabine against pancreatic cancer
Authors: Joanna Le, Hong Gao, Yi Le, William Richards, Scott Radig, Ronald Bleday, Thomas Clancy, Zhenglun Zhu
Journal: Cancer Research (2023)

Abstract Pancreatic ductal adenocarcinoma (PDA) is a lethal malignancy with median survival of less than one year and overall 5-year survival less than 5%. Gemcitabine has been the cornerstone in PDA treatment, yet its efficacy remains limited. Over the past decades, extensive investigations suggested a role of tumor microenvironment (TME) in rendering PDA resistance to gemcitabine, however, its underlying mechanism remained largely unknown. Cellular profiling has revealed the macrophages as a major immune cell component of PDA-TME. Our recent study showed that the expression of the homeobox protein VentX, a master regulator of macrophage plasticity, is significantly down-regulated in tumor associated macrophages (TAMs) of PDA. We demonstrated that restoration of VentX expression in PDA-TAMs polarizes the TAMs from a pro-tumor M2-like phenotype to an anti-tumor M1-like phenotype. We showed further that VentX-regulated-TAMs (VentX-TAMs) revert immune suppression of PDA-TME by inhibiting CD4 Treg differentiation and by promoting CD8 proliferation and activation. Using a newly developed tumor immune microenvironment-enabling model system (TIME-EMS), we showed that VentX-TAMs drastically promote efficacy of gemcitabine against PDA for about 4-fold but not cytotoxicity on normal pancreatic tissue. As such, our data suggested a function of VentX-TAMs to promote chemosensitivity of gemcitabine and to improve PDA prognosis. Citation Format: Joanna Le, Hong Gao, Yi Le, William Richards, Scott Radig, Ronald Bleday, Thomas Clancy, Zhenglun Zhu. VentX-modulated tumor associated macrophages revert immune suppression in tumor microenvironment and promote efficacy of gemcitabine against pancreatic cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5111.
Abstract 6701: 6-color Crystal Digital PCR for the high-plex detection of 10 <i>ESR1</i> mutations in breast cancer
Authors: Stavroula Smilkou, Aliki Ntzifa, Dimitra Stergiopoulou, Quentin Blache, Myrtille Remy, Cecile Jovelet, Allison Mallory, Evi Lianidou
Journal: Cancer Research (2023)

Abstract Introduction. ESR1 mutations have emerged as a key mechanism of resistance to endocrine therapy in estrogen-receptor-positive (ER+) breast cancer, thus detection of ESR1 mutations is crucial to monitor during patient treatment. We evaluated a novel 12plex breast cancer assay for the detection of 10 ESR1 mutations and AKT1 E17K in plasma cell-free DNA (cfDNA) using 6-color Crystal Digital PCRTM (naica® system, Stilla Technologies, France). We further compared the results with our previously reported ESR1 NAPA assay for D538G, Y537S, Y537C and Y537N mutations (Stergiopoulou et al, Cancers, 2021). Patients and Methods. Using the 6-color Crystal Digital PCRTM breast cancer 12plex assay, we analyzed 35 plasma cfDNA samples from ER+ breast cancer patients and 10 plasma cfDNA from healthy donors (HD). We also analyzed the same cfDNA samples using the ESR1 NAPA assay. Results. The Stilla 6-color breast cancer assay revealed in 5/35 (14,3%) ER+ cfDNA samples the AKT1_E17K and ESR1 D538G mutations. ESR1 D538G was detected in 4/35 ER+ cfDNA samples with the ESR1 NAPA assay. Direct comparison between Crystal Digital PCR™ and the ESR1 NAPA assay revealed a high concordance (97.1%) for 34/35 samples tested, for the detection of the D538G mutation, and with a higher sensitivity for the Stilla 6-color breast cancer assay. The ESR1 mutations Y537S, Y537C and Y537N were not detected by either method in any of the plasma-cfDNA samples. No AKT1 E17K or ESR1 mutations were detected in cfDNA from HD plasma. Conclusions. The naica® system 12plex ESR1 assay is quantitative, highly sensitive and easy to perform using plasma-cfDNA samples. The use of highly multiplexed Crystal Digital PCR™ shows great promise for clinical utility for ER+ breast cancer patient monitoring. Key words: Circulating tumor DNA; Crystal Digital PCR™, ESR1 mutations; liquid biopsy; mutation monitoring, 6-color multiplexing; Citation Format: Stavroula Smilkou, Aliki Ntzifa, Dimitra Stergiopoulou, Quentin Blache, Myrtille Remy, Cecile Jovelet, Allison Mallory, Evi Lianidou. 6-color Crystal Digital PCR for the high-plex detection of 10 ESR1 mutations in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6701.